To cite maskBAD in publications use:

Dannemann, M. et al. (2009) Bioinformatics 25, 2772--2779.

Dannemann, M. et al. (2012) BMC Bioinformatics 13:56.

Corresponding BibTeX entries:

  @Article{,
    author = {Dannemann M and Lorenc A. and Hellmann I. and Khaitovich
      P. and Lachmann M.},
    title = {The effects of probe binding affinity differences on gene
      expression measurements and how to deal with them},
    journal = {Bioinformatics},
    year = {2009},
    volume = {25},
    pages = {2772--2779},
    month = {Nov},
  }

  @Article{,
    author = {Dannemann M and Lachmann M. and Lorenc A.},
    title = {'maskBAD' - a package to detect and remove Affymetrix
      probes with binding affinity differences},
    journal = {BMC Bioinformatics},
    year = {2012},
    volume = {13},
    pages = {56},
    month = {April},
  }